Variant report

Variant	rs1889532
Chromosome Location	chr1:155951502-155951503
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155951100-155951540	HCT-116	colon:	n/a	n/a
2	CEBPB	chr1:155951024-155951588	Hela-S3	cervix:	n/a	chr1:155951405-155951418 chr1:155951405-155951416
3	TBP	chr1:155951380-155951580	HepG2	liver:	n/a	n/a
4	MYC	chr1:155951030-155951520	K562	blood:	n/a	n/a
5	POLR2A	chr1:155950858-155951651	Raji	blood:	n/a	n/a
6	CEBPB	chr1:155951098-155951616	IMR90	lung:	n/a	chr1:155951405-155951418 chr1:155951405-155951416
7	CEBPB	chr1:155951217-155951601	HepG2	liver:	n/a	chr1:155951405-155951418 chr1:155951405-155951416
8	CEBPB	chr1:155951083-155951589	K562	blood:	n/a	chr1:155951405-155951418 chr1:155951405-155951416
9	POLR2A	chr1:155951148-155951566	SK-N-SH	brain:	n/a	n/a
10	FOXP2	chr1:155951080-155951543	PFSK-1	brain:	n/a	n/a
11	MAZ	chr1:155951432-155951557	Hela-S3	cervix:	n/a	n/a
12	ARID3A	chr1:155951332-155951518	HepG2	liver:	n/a	n/a
13	FOS	chr1:155951101-155951521	HUVEC	blood vessel:	n/a	chr1:155951336-155951344 chr1:155951334-155951346 chr1:155951337-155951348 chr1:155951334-155951345
14	SMC3	chr1:155951271-155951573	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:155943832-155953868	U87	brain:	n/a	n/a
16	POLR2A	chr1:155943838-155953803	U87	brain:	n/a	n/a
17	RCOR1	chr1:155950602-155951968	IMR90	lung:	n/a	n/a
18	CEBPD	chr1:155951253-155951504	HepG2	liver:	n/a	n/a
19	CTCF	chr1:155951360-155951510	HBMEC	blood vessel:	n/a	n/a
20	CTCF	chr1:155951420-155951570	HPF	lung:	n/a	n/a
21	MXI1	chr1:155951234-155951553	HepG2	liver:	n/a	n/a
22	CEBPB	chr1:155951236-155951588	HepG2	liver:	n/a	chr1:155951405-155951418 chr1:155951405-155951416
23	CEBPB	chr1:155951288-155951531	HepG2	liver:	n/a	chr1:155951405-155951418 chr1:155951405-155951416
24	MTA3	chr1:155943968-155951505	GM12878	blood:	n/a	n/a
25	EBF1	chr1:155951494-155951780	GM12878	blood:	n/a	chr1:155951631-155951642
26	PBX3	chr1:155951139-155951562	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr1:155950620-155953675	U87	brain:	n/a	n/a
28	CTCF	chr1:155951480-155951630	HVMF	connective:	n/a	n/a
29	EBF1	chr1:155951437-155951834	GM12878	blood:	n/a	chr1:155951631-155951642
30	JUND	chr1:155951283-155951508	HepG2	liver:	n/a	chr1:155951336-155951344 chr1:155951334-155951346 chr1:155951334-155951345 chr1:155951337-155951348
31	POLR2A	chr1:155951008-155952442	IMR90	lung:	n/a	n/a
32	POLR2A	chr1:155951285-155951536	Hela-S3	cervix:	n/a	n/a
33	CEBPB	chr1:155951233-155951562	HepG2	liver:	n/a	chr1:155951405-155951418 chr1:155951405-155951416

No.	Distal block	Cell Line	Cell type
1	chr1:155949796..155952552-chr1:155965879..155967934,2	K562	blood:
2	chr1:155928147..155930680-chr1:155950511..155952920,2	K562	blood:
3	chr1:155950120..155952979-chr1:155958659..155960615,3	MCF-7	breast:
4	chr1:155943579..155945946-chr1:155950039..155953037,2	MCF-7	breast:
5	chr1:155949794..155952659-chr1:155990728..155992643,2	K562	blood:
6	chr1:155949831..155952126-chr1:156022990..156025068,2	K562	blood:
7	chr1:155907837..155914260-chr1:155947632..155952579,11	MCF-7	breast:
8	chr1:155903867..155905508-chr1:155950424..155952839,2	MCF-7	breast:
9	chr1:155950273..155951784-chr1:155982062..155983616,2	K562	blood:
10	chr1:155950118..155953012-chr1:155973513..155975361,2	K562	blood:
11	chr1:155906141..155908097-chr1:155950003..155952687,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RXFP4-2	chr1:155950658-155952777	ENSG00000273002.1

Variant related genes	Relation type
ARHGEF2	TF binding region
ENSG00000132680	Chromatin interaction
ENSG00000173080	Chromatin interaction
ENSG00000163479	Chromatin interaction
ENSG00000116586	Chromatin interaction
ENSG00000160803	Chromatin interaction
ENSG00000116584	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10796955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10908483	0.80[AMR][1000 genomes]
rs1111102	0.86[CEU][hapmap]
rs11264422	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11264426	1.00[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11585845	1.00[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12026057	0.84[AMR][1000 genomes]
rs12037177	0.95[CEU][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes]
rs12118795	0.90[CEU][hapmap];0.85[CHD][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs12144175	0.81[AMR][1000 genomes]
rs12568523	0.95[CEU][hapmap]
rs1749405	0.80[CHB][hapmap]
rs1889533	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2016251	0.95[CEU][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes]
rs2282301	0.95[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes]
rs2297649	0.95[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2364403	0.81[MEX][hapmap]
rs2993207	0.80[CHB][hapmap]
rs3820594	0.86[MEX][hapmap]
rs3856261	0.88[JPT][hapmap]
rs4661175	0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4661217	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4661218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs488079	0.80[CHB][hapmap]
rs490498	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs539602	0.80[CHB][hapmap]
rs61813286	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625658	0.80[CHB][hapmap]
rs6427297	0.81[CEU][hapmap]
rs66466805	0.82[AMR][1000 genomes]
rs6667652	0.95[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes]
rs6670477	0.80[AMR][1000 genomes]
rs6670493	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696019	0.95[CEU][hapmap];0.80[AMR][1000 genomes]
rs670523	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs72708205	0.81[AMR][1000 genomes]
rs7521292	0.81[AMR][1000 genomes]
rs7534858	1.00[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7545308	0.80[AMR][1000 genomes]
rs822478	0.89[JPT][hapmap]
rs867548	0.82[AMR][1000 genomes]
rs867549	0.95[CEU][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes]
rs867550	0.95[CEU][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes]
rs915178	0.86[CEU][hapmap]
rs915181	0.95[CEU][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes]
rs928596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1889532	RIT1	cis	cerebellum	SCAN
rs1889532	ROBLD3	cis	parietal	SCAN
rs1889532	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs1889532	PRUNE	cis	cerebellum	SCAN
rs1889532	YY1AP1	cis	cerebellum	SCAN
rs1889532	SPRR3	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155948600-155951600	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr1:155948600-155951600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
3	chr1:155948600-155951800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr1:155948600-155952000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr1:155948600-155952200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:155948600-155952200	Flanking Active TSS	Hela-S3	cervix
7	chr1:155948600-155953800	Flanking Active TSS	NHEK	skin
8	chr1:155948800-155951600	Flanking Active TSS	Primary B cells from peripheral blood	blood
9	chr1:155948800-155951800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr1:155948800-155953200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:155949000-155951600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr1:155949000-155951800	Enhancers	Liver	Liver
13	chr1:155949000-155952000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:155949000-155952000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr1:155949000-155952600	Flanking Active TSS	HSMMtube	muscle
16	chr1:155949000-155953400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:155949000-155953800	Weak transcription	Pancreas	Pancrea
18	chr1:155949200-155951600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr1:155949200-155952000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:155949200-155952000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr1:155949200-155953400	Weak transcription	Brain Germinal Matrix	brain
22	chr1:155949200-155953800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:155949400-155951600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:155949400-155951800	Enhancers	Brain Substantia Nigra	brain
25	chr1:155949400-155951800	Enhancers	Stomach Mucosa	stomach
26	chr1:155949400-155952000	Enhancers	Fetal Kidney	kidney
27	chr1:155949400-155953000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr1:155949400-155953000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:155949400-155953400	Flanking Active TSS	NHLF	lung
30	chr1:155949400-155953800	Enhancers	HUVEC	blood vessel
31	chr1:155949600-155951600	Flanking Active TSS	K562	blood
32	chr1:155949600-155951800	Enhancers	H1 Cell Line	embryonic stem cell
33	chr1:155949600-155951800	Enhancers	Fetal Intestine Large	intestine
34	chr1:155949600-155951800	Enhancers	Right Ventricle	heart
35	chr1:155949600-155952000	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr1:155949600-155952000	Genic enhancers	Fetal Stomach	stomach
37	chr1:155949600-155952000	Enhancers	Small Intestine	intestine
38	chr1:155949600-155952000	Flanking Active TSS	GM12878-XiMat	blood
39	chr1:155949600-155952600	Enhancers	Esophagus	oesophagus
40	chr1:155949600-155952600	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr1:155949600-155954200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr1:155949600-155954200	Enhancers	Fetal Lung	lung
43	chr1:155949600-155954400	Enhancers	Lung	lung
44	chr1:155949600-155954800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:155949600-155954800	Enhancers	Fetal Thymus	thymus
46	chr1:155949800-155951600	Enhancers	Brain Anterior Caudate	brain
47	chr1:155949800-155951800	Genic enhancers	Fetal Intestine Small	intestine
48	chr1:155949800-155951800	Enhancers	Thymus	Thymus
49	chr1:155949800-155952000	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr1:155949800-155952000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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